Said Section 18 (6) reads as follows:
"In case of supply of capital goods or plant and machinery, on which input tax credit has been taken, the registered person shall pay an amount equal to the input tax credit taken on the said capital goods or plant and machinery reduced by such percentage points as may be prescribed or the tax on the transaction value of such capital goods or plant and machinery determined under section 15, whichever is higher:
Provided that where refractory bricks, moulds and dies, jigs and fixtures are supplied as scrap, the taxable person may pay tax on the transaction value of such goods determined under section 15."
Rule 40 (2) of the CGST Rules, 2017 reads as follows:
"The amount of credit in the case of supply of capital goods or plant and machinery, for the purposes of sub-section (6) of section 18, shall be calculated by reducing the input tax on the said goods at the rate of five percentage points for every quarter or part thereof from the date of the issue of the invoice for such goods."
My understanding from above section and rule:
A. One needs to pay GST and need not reverse any ITC as per Section 18 (6) read with Rule 40 (2).
B. Quantum of gst payable is "the input tax credit taken on the said capital goods or plant and machinery reduced at the rate of five percentage points for every quarter or part thereof from the date of the issue of the invoice for such goods" OR "The tax on the transaction value of such capital goods or plant and machinery determined under section 15", whichever is higher
C. Calculation of GST payable - as mentioned in Para B - does not apply when 'refractory bricks, moulds and dies, jigs and fixtures' are supplied as 'scrap'.
Now, let's read Rule 44 (6) which is as follows:
"The amount of input tax creditfor the purposes of sub-section (6) of section 18 relating to capital goods shall be determined in the same manner as specified in clause (b) of sub-rule (1) and the amount shall be determined separately for input tax credit of central tax, State tax, Union territory tax and integrated tax:
Provided that where the amount so determined is more than the tax determined on the transaction value of the capital goods, the amount determined shall form part of the output tax liability and the same shall be furnished in FORM GSTR-1."
My understanding of said Rule 44 (6):
I. Even though heading of Rule 44 is 'Manner of reversal of credit under special circumstances', sub-rule (2) talks about determination of ITC for the purposes of sub-section (6) of section 18 and as said before, Section 18 (6) does not talk about 'ITC reversal' but talks about liability to pay GST at the time of supply of capital goods.
II. Proviso in sub-rule (6) of Rule 44 makes it more clear that it is dealing with the quantum of GST payable at the time of supply of capital goods and NOT talking about ITC to be reversed.
LASTLY:
There seems an apparent dichotomy between Rule 40 (2) and 44 (6). To avoid disputes / litigation etc. and till better clarity emerges through Board circulars / court rulings, it is better to pay taxes on higher side (i.e. 'Taxes calculated as per Section 18 (6) read with Rule 40 (2)' OR 'Taxes calculated as per Section 18 (6) read with Rule 44 (6)' whichever is higher). This is more so when the buyer is eligible to avail ITC against taxes so charged.
In any case, one needs NOT reverse any ITC as paying taxes against supply - as suggested above - is sufficient compliance with legal provisions in my view. In other words and in my view, 'paying such taxes at the time of supply of capital goods' is nothing but 'ITC reversal as envisioned in these rules' and there is no need to make such payment / reversal twice.
All above are strictly personal views of mine and the same should not be construed as professional advice / suggestion in any way.